By seniority, Justice Thomas would serve in an acting capacity if Chief Justice Roberts recused.
If Roberts were to resign, POTUS could nominate/appoint a replacement Chief – either one of the current Associate Justices or a new addition to the Court. That scenario would likely be met with demands for a promise to recuse given that the new Justice would be nominated by the Prez who'd be tried. And that would mean going back to the acting Chief – Thomas by seniority, anyway.
So it would be Associate Justice Thomas as acting Chief (who could also be elevated as the new Chief Justice if Roberts resigned).